Calcium in PDB 5dzv: Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5

The structure of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5, PDB code: 5dzv was solved by K.M.Goodman, F.Bahna, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.31 / 3.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.440, 106.450, 558.829, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 29

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 (pdb code 5dzv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5, PDB code: 5dzv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:56.7 occ:1.00 OE2 A:GLU8 2.2 61.2 1.0 OE2 A:GLU64 2.4 0.9 1.0 OD1 A:ASP99 2.5 75.2 1.0 OD1 A:ASP96 2.5 99.9 1.0 O A:ILE97 2.5 91.2 1.0 OD1 A:ASP132 2.6 0.2 1.0 CG A:ASP96 3.3 96.4 1.0 CD A:GLU8 3.4 84.4 1.0 CG A:ASP99 3.5 67.4 1.0 CD A:GLU64 3.6 0.1 1.0 C A:ILE97 3.7 68.0 1.0 OD2 A:ASP96 3.7 0.2 1.0 CG A:ASP132 3.7 88.3 1.0 N A:ILE97 3.9 77.0 1.0 OE1 A:GLU8 3.9 91.9 1.0 OD1 A:ASN100 3.9 93.3 1.0 OD2 A:ASP99 4.0 68.5 1.0 OE1 A:GLU64 4.1 0.2 1.0 N A:ASP99 4.1 72.6 1.0 NH2 A:ARG63 4.3 0.5 1.0 NE A:ARG63 4.3 0.1 1.0 CA A:ILE97 4.4 99.0 1.0 CA A:ASP132 4.4 1.0 1.0 CB A:ASP96 4.5 71.3 1.0 CB A:ASP132 4.5 93.7 1.0 CA A:CA603 4.5 85.0 1.0 OD2 A:ASP132 4.6 66.5 1.0 CG A:GLU8 4.6 67.6 1.0 C A:ASP96 4.6 55.3 1.0 CA A:ASP96 4.6 54.8 1.0 N A:ASN98 4.7 69.1 1.0 CB A:ASP99 4.7 82.2 1.0 CG2 A:ILE97 4.7 61.1 1.0 N A:ASN100 4.8 57.0 1.0 CA A:ASN98 4.8 64.9 1.0 CG A:GLU64 4.8 0.8 1.0 CZ A:ARG63 4.8 0.3 1.0 CA A:ASP99 4.9 93.3 1.0 CG A:ASN100 4.9 86.7 1.0 C A:ASN98 5.0 62.8 1.0

Calcium binding site 2 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:95.2 occ:1.00 OD2 A:ASP130 2.4 0.2 1.0 O A:ASN136 2.5 93.9 1.0 OD1 A:ASP130 2.6 0.2 1.0 OD2 A:ASP132 2.7 66.5 1.0 CG A:ASP130 2.7 0.2 1.0 O A:ASN100 2.8 53.0 1.0 OD2 A:ASP187 2.8 82.3 1.0 OD1 A:ASN98 3.3 58.8 1.0 CB A:ASP132 3.4 93.7 1.0 CG A:ASP132 3.4 88.3 1.0 CG A:ASP187 3.6 82.4 1.0 C A:ASN136 3.7 0.9 1.0 CB A:ASP187 3.8 54.9 1.0 C A:ASN100 4.0 59.0 1.0 CB A:ASP130 4.1 99.0 1.0 CA A:ALA137 4.1 0.0 1.0 N A:ALA137 4.4 0.8 1.0 CG A:ASN98 4.4 78.1 1.0 CD A:PRO102 4.5 57.5 1.0 OD1 A:ASP132 4.6 0.2 1.0 N A:PRO102 4.6 94.3 1.0 CA A:ASP132 4.6 1.0 1.0 N A:LEU138 4.7 0.7 1.0 C A:PRO101 4.7 97.0 1.0 OD1 A:ASP187 4.7 0.7 1.0 N A:ASP132 4.7 0.4 1.0 C A:ALA137 4.7 0.8 1.0 CG A:PRO102 4.8 56.8 1.0 CA A:PRO101 4.8 70.9 1.0 CB A:ASN136 4.8 0.8 1.0 CA A:ASN136 4.8 1.0 1.0 N A:PRO101 4.9 77.5 1.0 ND2 A:ASN98 4.9 86.8 1.0

Calcium binding site 3 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:85.0 occ:1.00 OE2 A:GLU9 2.4 1.0 1.0 OE1 A:GLU64 2.5 0.2 1.0 OD2 A:ASP99 2.6 68.5 1.0 OE1 A:GLU8 2.8 91.9 1.0 OD1 A:ASP62 2.8 0.5 1.0 CD A:GLU64 3.3 0.1 1.0 CD A:GLU9 3.3 94.2 1.0 CG A:ASP99 3.6 67.4 1.0 OE2 A:GLU64 3.6 0.9 1.0 CD A:GLU8 3.7 84.4 1.0 CG A:ASP62 3.8 0.6 1.0 OD1 A:ASP99 3.8 75.2 1.0 OD1 A:ASN100 3.9 93.3 1.0 OE1 A:GLU9 4.0 0.1 1.0 OE2 A:GLU8 4.1 61.2 1.0 CG A:GLU9 4.1 89.4 1.0 OD2 A:ASP62 4.4 0.8 1.0 N A:ARG63 4.5 81.7 1.0 CA A:CA601 4.5 56.7 1.0 CG A:GLU64 4.5 0.8 1.0 CA A:ASP62 4.6 0.3 1.0 NH2 A:ARG60 4.6 77.6 1.0 N A:GLU64 4.7 0.7 1.0 CB A:ASP62 4.8 0.7 1.0 CB A:GLU64 4.8 0.9 1.0 CG A:GLU8 4.8 67.6 1.0 C A:ASP62 4.9 0.0 1.0 CB A:ASP99 4.9 82.2 1.0 CG A:ASN100 5.0 86.7 1.0

Calcium binding site 4 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:73.1 occ:1.00 OD1 A:ASP205 2.5 0.7 1.0 OE1 A:GLU115 2.5 0.2 1.0 OE2 A:GLU174 2.7 84.7 1.0 OD1 A:ASP208 2.8 0.6 1.0 O A:VAL206 2.8 97.7 1.0 OD1 A:ASP241 2.9 0.9 1.0 OE2 A:GLU115 3.2 0.9 1.0 CD A:GLU115 3.2 0.8 1.0 OE1 A:GLU174 3.4 90.1 1.0 OD1 A:ASN209 3.4 0.5 1.0 CD A:GLU174 3.4 98.8 1.0 CG A:ASP205 3.7 0.7 1.0 N A:VAL206 3.8 92.5 1.0 CA A:CA606 3.8 0.6 1.0 C A:VAL206 3.8 0.9 1.0 CG A:ASP208 3.9 0.1 1.0 CG A:ASP241 4.0 0.5 1.0 OD2 A:ASP208 4.3 97.9 1.0 CA A:VAL206 4.4 0.1 1.0 N A:ASP208 4.5 0.6 1.0 OD2 A:ASP205 4.5 0.9 1.0 OD1 A:ASP172 4.5 0.3 1.0 CG A:ASN209 4.5 0.6 1.0 CA A:ASP205 4.5 0.5 1.0 C A:ASP205 4.6 0.1 1.0 CB A:ASP205 4.7 0.8 1.0 CB A:ARG173 4.7 0.0 1.0 CG A:GLU115 4.7 88.5 1.0 CB A:ASP241 4.8 0.8 1.0 OD2 A:ASP241 4.8 0.4 1.0 N A:ASN207 4.9 0.1 1.0 CA A:ASP241 4.9 0.4 1.0 CG A:GLU174 4.9 0.3 1.0 O A:LEU240 5.0 0.9 1.0

Calcium binding site 5 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:0.1 occ:1.00 OD2 A:ASP241 2.3 0.4 1.0 OD1 A:ASN207 2.5 0.7 1.0 O A:ASN245 2.6 0.1 1.0 OD2 A:ASP239 2.6 0.9 1.0 O A:ASN209 2.7 1.0 1.0 OD2 A:ASP295 2.9 0.7 1.0 OD1 A:ASP239 3.1 0.0 1.0 CG A:ASP239 3.2 0.3 1.0 CG A:ASP241 3.3 0.5 1.0 CG A:ASN207 3.6 0.7 1.0 CG A:ASP295 3.7 0.7 1.0 C A:ASN245 3.7 0.9 1.0 CB A:ASP241 3.7 0.8 1.0 C A:ASN209 3.9 0.7 1.0 CB A:ASP295 4.1 0.3 1.0 ND2 A:ASN207 4.2 0.1 1.0 CA A:ASN245 4.4 93.7 1.0 CB A:ASN245 4.4 0.2 1.0 OD1 A:ASP241 4.4 0.9 1.0 OD1 A:ASP295 4.6 0.7 1.0 CA A:ASN209 4.7 0.0 1.0 CB A:ASP239 4.7 0.4 1.0 N A:ASN209 4.7 0.9 1.0 CB A:ASN207 4.7 94.7 1.0 CB A:ASN209 4.8 0.6 1.0 N A:GLY246 4.8 0.7 1.0 N A:ALA210 4.9 90.5 1.0 CA A:ASN207 4.9 0.4 1.0 CD A:PRO211 4.9 0.8 1.0 N A:ASP241 5.0 0.8 1.0 CA A:ASP241 5.0 0.4 1.0

Calcium binding site 6 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:0.6 occ:1.00 OE2 A:GLU115 2.2 0.9 1.0 OD1 A:ASP172 2.6 0.3 1.0 OD2 A:ASP208 2.6 97.9 1.0 OD1 A:ASP208 3.1 0.6 1.0 CG A:ASP208 3.2 0.1 1.0 CG A:ASP172 3.2 0.8 1.0 OD1 A:ASN209 3.2 0.5 1.0 OD2 A:ASP172 3.3 0.5 1.0 CD A:GLU115 3.4 0.8 1.0 OE1 A:GLU174 3.5 90.1 1.0 CA A:CA604 3.8 73.1 1.0 OE1 A:GLU115 4.0 0.2 1.0 CD A:GLU174 4.1 98.8 1.0 CG A:ASN209 4.1 0.6 1.0 OE2 A:GLU174 4.3 84.7 1.0 ND2 A:ASN209 4.3 0.5 1.0 CG A:GLU115 4.5 88.5 1.0 CB A:ASP172 4.6 0.9 1.0 CB A:ASP208 4.7 0.7 1.0

Calcium binding site 7 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:0.7 occ:1.00 OD1 A:ASP313 2.5 0.3 1.0 OE1 A:GLU224 2.6 0.1 1.0 OE2 A:GLU224 2.8 0.3 1.0 OE2 A:GLU282 2.9 0.8 1.0 CD A:GLU224 3.0 0.8 1.0 O A:ALA314 3.2 0.2 1.0 OE1 A:GLU282 3.3 1.0 1.0 OD1 A:ASP316 3.3 0.7 1.0 CA A:CA608 3.4 0.2 1.0 OD1 A:ASP349 3.4 0.3 1.0 CD A:GLU282 3.5 0.5 1.0 CG A:ASP313 3.5 1.0 1.0 N A:ALA314 3.7 0.1 1.0 CB A:PHE281 3.8 0.5 1.0 CA A:ASP313 4.0 0.2 1.0 C A:ALA314 4.2 0.7 1.0 CG A:ASP316 4.2 0.6 1.0 C A:ASP313 4.2 0.9 1.0 OD2 A:ASP313 4.3 0.9 1.0 CB A:ASP313 4.3 0.9 1.0 OD1 A:ASP280 4.4 0.4 1.0 OD2 A:ASP316 4.4 0.5 1.0 CG A:GLU224 4.5 0.8 1.0 CG A:ASP349 4.5 0.5 1.0 CA A:ALA314 4.5 0.0 1.0 N A:PHE281 4.6 0.1 1.0 CG A:PHE281 4.7 0.2 1.0 CD2 A:PHE281 4.8 0.1 1.0 CA A:PHE281 4.8 0.2 1.0 CG A:GLU282 4.9 0.4 1.0 N A:GLU282 5.0 0.3 1.0

Calcium binding site 8 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:0.2 occ:1.00 OD2 A:ASP316 2.3 0.5 1.0 OD1 A:ASP280 2.3 0.4 1.0 OE2 A:GLU224 2.4 0.3 1.0 OD1 A:ASP316 2.9 0.7 1.0 CG A:ASP316 2.9 0.6 1.0 OE1 A:GLU282 3.0 1.0 1.0 CG A:ASP280 3.1 0.5 1.0 OD2 A:ASP280 3.3 1.0 1.0 CA A:CA607 3.4 0.7 1.0 CD A:GLU224 3.6 0.8 1.0 ND2 A:ASN317 3.7 0.7 1.0 CD A:GLU282 3.7 0.5 1.0 OE2 A:GLU282 3.9 0.8 1.0 OE1 A:GLU224 4.2 0.1 1.0 CB A:ASP316 4.4 0.4 1.0 CG A:ASN317 4.4 0.3 1.0 CB A:ASP280 4.6 0.3 1.0 OD1 A:ASN317 4.6 0.8 1.0 CG A:GLU224 4.7 0.8 1.0 OD1 A:ASP349 4.9 0.3 1.0

Calcium binding site 9 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:0.4 occ:1.00 OD2 A:ASP400 2.2 0.2 1.0 OD2 A:ASP349 2.3 0.4 1.0 O A:ASN317 2.5 0.1 1.0 OD1 A:ASP347 2.5 0.0 1.0 OD2 A:ASP347 2.8 0.5 1.0 ND2 A:ASN315 3.0 0.7 1.0 O A:ASN353 3.0 0.7 1.0 CG A:ASP347 3.0 0.1 1.0 CG A:ASP349 3.0 0.5 1.0 CB A:ASP349 3.1 0.7 1.0 CG A:ASP400 3.4 0.6 1.0 C A:ASN317 3.7 0.5 1.0 OD1 A:ASP400 4.0 0.8 1.0 N A:ASP349 4.2 0.4 1.0 OD1 A:ASP349 4.2 0.3 1.0 C A:ASN353 4.2 0.9 1.0 CA A:ASP349 4.2 0.5 1.0 CG A:ASN315 4.2 0.2 1.0 CA A:ASN317 4.5 0.6 1.0 CB A:ASP347 4.5 0.9 1.0 CD A:PRO319 4.5 0.9 1.0 CB A:ASN317 4.6 0.5 1.0 N A:ASN317 4.6 0.2 1.0 N A:PRO319 4.6 0.6 1.0 CB A:ASP400 4.6 0.7 1.0 CG A:PRO319 4.6 0.2 1.0 N A:ALA318 4.7 0.6 1.0 C A:ALA318 4.7 0.5 1.0 CB A:ASN353 4.7 0.0 1.0 CA A:ALA318 4.8 0.4 1.0 OD1 A:ASN315 4.9 0.7 1.0

Calcium binding site 10 out of 24 in the Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin Alpha 7 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:0.4 occ:1.00 OD1 A:ASP418 2.5 0.2 1.0 O A:VAL419 2.6 0.0 1.0 OE1 A:GLU332 2.8 0.8 1.0 CA A:CA611 2.8 0.7 1.0 OE2 A:GLU387 2.9 0.9 1.0 N A:VAL419 3.1 0.3 1.0 OD1 A:ASP421 3.2 0.9 1.0 OE1 A:GLU387 3.3 1.0 1.0 CD A:GLU387 3.5 0.9 1.0 C A:VAL419 3.5 0.9 1.0 CG A:ASP418 3.7 0.8 1.0 CB A:ARG386 3.7 0.6 1.0 CA A:VAL419 3.8 0.3 1.0 OD1 A:ASP454 3.8 1.0 1.0 CD A:GLU332 4.0 0.1 1.0 CG A:ASP421 4.0 0.0 1.0 C A:ASP418 4.1 0.9 1.0 CA A:ASP418 4.1 0.6 1.0 CG A:ARG386 4.2 0.9 1.0 OD2 A:ASP421 4.3 0.0 1.0 CB A:VAL419 4.4 0.4 1.0 CG A:ASP454 4.4 0.2 1.0 CB A:ASP418 4.5 0.8 1.0 OE2 A:GLU332 4.5 0.3 1.0 OD2 A:ASP418 4.6 0.6 1.0 N A:ASN420 4.7 0.2 1.0 ND2 A:ASN422 4.7 0.2 1.0 N A:ASP421 4.8 0.2 1.0 CA A:ARG386 5.0 0.3 1.0 CG A:GLU387 5.0 0.3 1.0

K.M.Goodman, R.Rubinstein, C.A.Thu, F.Bahna, S.Mannepalli, G.Ahlsen, C.Rittenhouse, T.Maniatis, B.Honig, L.Shapiro. Structural Basis of Diverse Homophilic Recognition By Clustered Alpha- and Beta-Protocadherins. Neuron V. 90 709 2016.
ISSN: ISSN 0896-6273
PubMed: 27161523
DOI: 10.1016/J.NEURON.2016.04.004